Discovery of highly potent and ALK2/ALK1 selective kinase inhibitors using DNA-encoded chemistry technology

  • Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2413108121. doi: 10.1073/pnas.2413108121.
Ravikumar Jimmidi  #  1  2 ,  Diana Monsivais  #  1  2 ,  Hai Minh Ta  #  1  2 ,  Kiran L Sharma  1  2 ,  Kurt M Bohren  1  2 ,  Srinivas Chamakuri  1  2 ,  Zian Liao  1  2  3 ,  Feng Li  1  2  4 ,  John M Hakenjos  1  2 ,  Jian-Yuan Li  1  2 ,  Yuji Mishina  5 ,  Haichun Pan  5 ,  Xuan Qin  1  2 ,  Matthew B Robers  6 ,  Banumathi Sankaran  7 ,  Zhi Tan  1  2  8 ,  Suni Tang  1  2 ,  Yasmin M Vasquez  1  2 ,  Jennifer Wilkinson  6 ,  Damian W Young  1  2  8 ,  Stephen S Palmer  1  2 ,  Kevin R MacKenzie  1  2  8 ,  Choel Kim  1  2  8 ,  Martin M Matzuk  1  2  3  4  8
Affiliations
  • 1. Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030.
  • 2. Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030.
  • 3. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.
  • 4. Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030.
  • 5. Department of Biologic and Materials Science, School of Dentistry, University of Michigan, Ann Arbor, MI 48109.
  • 6. Promega Corporation, Madison, WI 53711.
  • 7. Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
  • 8. Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030.
  • # Contributed equally.
PMID: 39541346 DOI: 10.1073/pnas.2413108121
Abstract

Activin receptor type 1 (ACVR1; ALK2) and activin receptor like type 1 (ACVRL1; ALK1) are transforming growth factor beta family receptors that integrate extracellular signals of bone morphogenic proteins (BMPs) and activins into Mothers Against Decapentaplegic homolog 1/5 (SMAD1/SMAD5) signaling complexes. Several activating mutations in ALK2 are implicated in fibrodysplasia ossificans progressiva (FOP), diffuse intrinsic pontine gliomas, and ependymomas. The ALK2 R206H mutation is also present in a subset of endometrial tumors, melanomas, non-small lung cancers, and colorectal cancers, and ALK2 expression is elevated in pancreatic Cancer. Using DNA-encoded chemistry technology, we screened 3.94 billion unique compounds from our diverse DNA-encoded chemical libraries (DECLs) against the kinase domain of ALK2. Off-DNA synthesis of DECL hits and biochemical validation revealed nanomolar potent ALK2 inhibitors. Further structure-activity relationship studies yielded center for drug discovery (CDD)-2789, a potent [NanoBRET (NB) cell IC50: 0.54 μM] and metabolically stable analog with good pharmacological profile. Crystal structures of ALK2 bound with CDD-2281, CDD-2282, or CDD-2789 show that these inhibitors bind the active site through Van der Waals interactions and solvent-mediated hydrogen bonds. CDD-2789 exhibits high selectivity toward ALK2/ALK1 in KINOMEscan analysis and NB K192 assay. In cell-based studies, ALK2 inhibitors effectively attenuated Activin A and BMP-induced Phosphorylated SMAD1/5 activation in fibroblasts from individuals with FOP in a dose-dependent manner. Thus, CDD-2789 is a valuable tool compound for further investigation of the biological functions of ALK2 and ALK1 and the therapeutic potential of specific inhibition of ALK2.

Keywords
DEL; X-ray Crystallography; kinase inhibitors.
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